Merge branch 'Project-MONAI:dev' into dev

.github/workflows/chatops.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: dispatch
-        uses: peter-evans/slash-command-dispatch@v3.0.2
+        uses: peter-evans/slash-command-dispatch@v4.0.0
         with:
           token: ${{ secrets.PR_MAINTAIN }}
           reaction-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/cron-ngc-bundle.yml

@@ -26,7 +26,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ~/.cache/pip

.github/workflows/cron.yml

@@ -67,7 +67,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -111,7 +111,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -212,7 +212,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: false
         files: ./coverage.xml

.github/workflows/docker.yml

@@ -62,7 +62,7 @@ jobs:
     - name: docker_build
       shell: bash
       run: |
-        rm -rf /opt/hostedtoolcache
+        find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         docker --version
         # get tag info for versioning
         cat _version.py

.github/workflows/integration.yml

@@ -22,7 +22,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -71,7 +71,7 @@ jobs:
       run: ./runtests.sh --build --net
 
     - name: Add reaction
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}
@@ -95,7 +95,7 @@ jobs:
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -151,7 +151,7 @@ jobs:
         python -m tests.test_integration_gpu_customization
 
     - name: Add reaction
-      uses: peter-evans/create-or-update-comment@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         token: ${{ secrets.PR_MAINTAIN }}
         repository: ${{ github.event.client_payload.github.payload.repository.full_name }}

.github/workflows/pythonapp-gpu.yml

@@ -137,6 +137,6 @@ jobs:
       shell: bash
     - name: Upload coverage
       if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }}
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         files: ./coverage.xml

.github/workflows/pythonapp-min.yml

@@ -44,7 +44,7 @@ jobs:
         echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
@@ -90,7 +90,7 @@ jobs:
         echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
@@ -135,7 +135,7 @@ jobs:
         echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}

.github/workflows/pythonapp.yml

@@ -36,7 +36,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ~/.cache/pip
@@ -83,7 +83,7 @@ jobs:
         echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
       shell: bash
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
@@ -136,7 +136,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -217,7 +217,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |

.github/workflows/release.yml

@@ -27,7 +27,7 @@ jobs:
         python -m pip install --user --upgrade setuptools wheel
     - name: Build and test source archive and wheel file
       run: |
-        rm -rf /opt/hostedtoolcache
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         git fetch --depth=1 origin +refs/tags/*:refs/tags/*
         root_dir=$PWD
         echo "$root_dir"
@@ -102,7 +102,7 @@ jobs:
           python-version: '3.9'
       - shell: bash
         run: |
-          rm -rf /opt/hostedtoolcache
+          find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
           git describe
           python -m pip install --user --upgrade setuptools wheel
           python setup.py build
@@ -143,7 +143,7 @@ jobs:
           RELEASE_VERSION: ${{ steps.versioning.outputs.tag }}
         shell: bash
         run: |
-          rm -rf /opt/hostedtoolcache
+          find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
           # get tag info for versioning
           mv _version.py monai/
           # version checks

.github/workflows/setupapp.yml

@@ -35,7 +35,7 @@ jobs:
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
       if: ${{ startsWith(github.ref, 'refs/heads/dev') }}
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -68,7 +68,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -91,7 +91,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -100,7 +100,7 @@ jobs:
         key: ${{ runner.os }}-${{ matrix.python-version }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies
       run: |
-        rm -rf /opt/hostedtoolcache
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
         python -m pip install -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
@@ -111,7 +111,7 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -128,7 +128,7 @@ jobs:
       run: |
         echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
     - name: cache for pip
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       id: cache
       with:
         path: |
@@ -146,7 +146,7 @@ jobs:
     - name: Install the default branch with build (dev branch only)
       if: github.ref == 'refs/heads/dev'
       run: |
-        rm -rf /opt/hostedtoolcache
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         BUILD_MONAI=1 pip install git+https://github.com/Project-MONAI/MONAI#egg=MONAI
         python -c 'import monai; monai.config.print_config()'
     - name: Get the test cases (dev branch only)

monai/apps/datasets.py

@@ -737,6 +737,7 @@ def get_dataset(self, folds: Sequence[int] | int, **dataset_params: Any) -> obje
         dataset_params_.update(dataset_params)
 
         class _NsplitsDataset(self.dataset_cls):  # type: ignore
+
             def _split_datalist(self, datalist: list[dict]) -> list[dict]:
                 data = partition_dataset(data=datalist, num_partitions=nfolds, shuffle=True, seed=seed)
                 return select_cross_validation_folds(partitions=data, folds=folds)

monai/apps/deepedit/transforms.py

@@ -34,6 +34,7 @@
 
 
 class DiscardAddGuidanced(MapTransform):
+
     def __init__(
         self,
         keys: KeysCollection,
@@ -84,6 +85,7 @@ def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.nda
 
 
 class NormalizeLabelsInDatasetd(MapTransform):
+
     def __init__(
         self, keys: KeysCollection, label_names: dict[str, int] | None = None, allow_missing_keys: bool = False
     ):
@@ -121,6 +123,7 @@ def __call__(self, data: Mapping[Hashable, np.ndarray]) -> dict[Hashable, np.nda
 
 
 class SingleLabelSelectiond(MapTransform):
+
     def __init__(
         self, keys: KeysCollection, label_names: Sequence[str] | None = None, allow_missing_keys: bool = False
     ):

monai/apps/detection/metrics/coco.py

@@ -72,6 +72,7 @@
 
 
 class COCOMetric:
+
     def __init__(
         self,
         classes: Sequence[str],

monai/apps/detection/utils/ATSS_matcher.py

@@ -164,6 +164,7 @@ def compute_matches(
 
 
 class ATSSMatcher(Matcher):
+
     def __init__(
         self,
         num_candidates: int = 4,

monai/apps/detection/utils/anchor_utils.py

@@ -369,8 +369,12 @@ class AnchorGeneratorWithAnchorShape(AnchorGenerator):
     def __init__(
         self,
         feature_map_scales: Sequence[int] | Sequence[float] = (1, 2, 4, 8),
-        base_anchor_shapes: Sequence[Sequence[int]]
-        | Sequence[Sequence[float]] = ((32, 32, 32), (48, 20, 20), (20, 48, 20), (20, 20, 48)),
+        base_anchor_shapes: Sequence[Sequence[int]] | Sequence[Sequence[float]] = (
+            (32, 32, 32),
+            (48, 20, 20),
+            (20, 48, 20),
+            (20, 20, 48),
+        ),
         indexing: str = "ij",
     ) -> None:
         nn.Module.__init__(self)

monai/apps/pathology/transforms/post/array.py

@@ -162,7 +162,7 @@ def __call__(self, prob_map: NdarrayOrTensor) -> NdarrayOrTensor:
         pred = label(pred)[0]
         if self.remove_small_objects is not None:
             pred = self.remove_small_objects(pred)
-        pred[pred > 0] = 1  # type: ignore
+        pred[pred > 0] = 1
 
         return convert_to_dst_type(pred, prob_map, dtype=self.dtype)[0]
 
@@ -338,7 +338,7 @@ def __call__(self, mask: NdarrayOrTensor, instance_border: NdarrayOrTensor) -> N
         instance_border = instance_border >= self.threshold  # uncertain area
 
         marker = mask - convert_to_dst_type(instance_border, mask)[0]  # certain foreground
-        marker[marker < 0] = 0  # type: ignore
+        marker[marker < 0] = 0
         marker = self.postprocess_fn(marker)
         marker = convert_to_numpy(marker)
 
@@ -634,7 +634,7 @@ def __call__(  # type: ignore
 
         seg_map_crop = convert_to_dst_type(seg_map_crop == instance_id, type_map_crop, dtype=bool)[0]
 
-        inst_type = type_map_crop[seg_map_crop]  # type: ignore
+        inst_type = type_map_crop[seg_map_crop]
         type_list, type_pixels = unique(inst_type, return_counts=True)
         type_list = list(zip(type_list, type_pixels))
         type_list = sorted(type_list, key=lambda x: x[1], reverse=True)

monai/data/dataset.py

@@ -1275,6 +1275,7 @@ def __len__(self) -> int:
         return min(len(dataset) for dataset in self.data)
 
     def _transform(self, index: int):
+
         def to_list(x):
             return list(x) if isinstance(x, (tuple, list)) else [x]
 

monai/data/decathlon_datalist.py

@@ -24,13 +24,11 @@
 
 
 @overload
-def _compute_path(base_dir: PathLike, element: PathLike, check_path: bool = False) -> str:
-    ...
+def _compute_path(base_dir: PathLike, element: PathLike, check_path: bool = False) -> str: ...
 
 
 @overload
-def _compute_path(base_dir: PathLike, element: list[PathLike], check_path: bool = False) -> list[str]:
-    ...
+def _compute_path(base_dir: PathLike, element: list[PathLike], check_path: bool = False) -> list[str]: ...
 
 
 def _compute_path(base_dir, element, check_path=False):